We propose an automated needle hydrophone-based scanning system to measure high-resolution 3-D acoustic pressure distributions generated by high-intensity focused ultrasound (HIFU). The hardware consists of a host computer, subsystems for HIFU generation, and an oscilloscope to sample the pressure response from a sensor in a water tank. Software was developed to control the hardware subsystems, to search for the initial scan position, and to design the scanning path and volume. A preoperative scanning plan with three perpendicular planes is used to manipulate the position of the HIFU transducer and to automate the acquisition of the spatial acoustic pressure distribution. The post-processing process displays the scanning results, compensates time delays caused by continuous linear scans, and quantifies the focal region. A method to minimize the displacement error induced by the time delay improves the scanning speed of a conventional needle hydrophone-based scanning system. Moreover, a noise-robust, automatic-focus searching algorithm using Gaussian function fitting reduces the total number of iterations and prevents the initial scanning position search from diverging. Finally, the minimum-volume enclosing ellipsoid approximation is used to quantify the size and orientation of the 3-D focal region thresholded by the minimum pressure of interest for various input conditions and to test the reproducibility of the scanning system.